{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T12:17:51Z","timestamp":1775996271548,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T00:00:00Z","timestamp":1673568000000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Ministry for Education and Research","award":["031L0203A"],"award-info":[{"award-number":["031L0203A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Somatic mutations are usually called by analyzing the DNA sequence of a tumor sample in conjunction with a matched normal. However, a matched normal is not always available, for instance, in retrospective analysis or diagnostic settings. For such cases, tumor-only somatic variant calling tools need to be designed. Previously proposed approaches demonstrate inferior performance on whole-genome sequencing (WGS) samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present the convolutional neural network-based approach called DeepSom for detecting somatic single nucleotide polymorphism and short insertion and deletion variants in tumor WGS samples without a matched normal. We validate DeepSom by reporting its performance on five different cancer datasets. We also demonstrate that on WGS samples DeepSom outperforms previously proposed methods for tumor-only somatic variant calling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DeepSom is available as a GitHub repository at https:\/\/github.com\/heiniglab\/DeepSom.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac828","type":"journal-article","created":{"date-parts":[[2023,1,14]],"date-time":"2023-01-14T01:26:50Z","timestamp":1673659610000},"source":"Crossref","is-referenced-by-count":9,"title":["DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2609-1356","authenticated-orcid":false,"given":"Sergey","family":"Vilov","sequence":"first","affiliation":[{"name":"Institute of Computational Biology, Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany"}]},{"given":"Matthias","family":"Heinig","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany"},{"name":"Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich , 85748 Garching, Germany"},{"name":"DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich , 10785 Berlin , Germany"}]}],"member":"286","published-online":{"date-parts":[[2023,1,13]]},"reference":[{"key":"2023011709414124600_btac828-B1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"key":"2023011709414124600_btac828-B2","author":"Benjamin","year":"2019"},{"key":"2023011709414124600_btac828-B3","first-page":"281","article-title":"Random search for hyper-parameter optimization","volume":"13","author":"Bergstra","year":"2012","journal-title":"J. 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